Multiple sequence alignment - TraesCS4B01G320100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G320100 chr4B 100.000 2798 0 0 1 2798 611322043 611319246 0.000000e+00 5168
1 TraesCS4B01G320100 chr4D 85.767 1890 133 68 537 2378 481884355 481882554 0.000000e+00 1875
2 TraesCS4B01G320100 chr4D 89.625 453 39 6 1 450 498027627 498028074 1.120000e-158 569
3 TraesCS4B01G320100 chr4D 89.000 400 26 3 2399 2796 481882572 481882189 1.950000e-131 479
4 TraesCS4B01G320100 chr4D 91.007 278 20 4 1165 1438 211482126 211481850 1.220000e-98 370
5 TraesCS4B01G320100 chr5A 83.648 1957 121 82 523 2378 660836018 660837876 0.000000e+00 1657
6 TraesCS4B01G320100 chr5A 91.367 278 19 4 1165 1438 502528695 502528419 2.630000e-100 375
7 TraesCS4B01G320100 chr5A 85.542 332 26 9 2399 2718 660837858 660838179 7.470000e-86 327
8 TraesCS4B01G320100 chr5A 91.892 111 9 0 415 525 116699279 116699389 3.730000e-34 156
9 TraesCS4B01G320100 chr5A 91.892 111 9 0 415 525 116781263 116781373 3.730000e-34 156
10 TraesCS4B01G320100 chr2D 90.548 529 41 8 1 525 121722257 121722780 0.000000e+00 691
11 TraesCS4B01G320100 chr1D 89.225 529 50 6 1 526 342160013 342160537 0.000000e+00 654
12 TraesCS4B01G320100 chr1D 88.847 529 53 4 2 527 458289702 458289177 0.000000e+00 645
13 TraesCS4B01G320100 chr1D 86.517 534 56 12 1 527 20720719 20720195 8.690000e-160 573
14 TraesCS4B01G320100 chr7A 86.717 527 57 12 1 525 31059935 31060450 8.690000e-160 573
15 TraesCS4B01G320100 chr7A 87.633 469 50 8 1 464 1513680 1513215 3.170000e-149 538
16 TraesCS4B01G320100 chr7A 93.991 233 14 0 1206 1438 676070004 676069772 1.230000e-93 353
17 TraesCS4B01G320100 chr6D 86.142 534 60 11 1 525 725002 724474 5.230000e-157 564
18 TraesCS4B01G320100 chr2A 86.064 531 63 8 1 525 696186238 696185713 6.770000e-156 560
19 TraesCS4B01G320100 chr5D 91.007 278 20 4 1165 1438 498728551 498728827 1.220000e-98 370
20 TraesCS4B01G320100 chr5D 90.000 80 6 2 2592 2669 495490159 495490080 4.930000e-18 102
21 TraesCS4B01G320100 chr1B 89.789 284 24 4 1159 1438 665253011 665252729 2.650000e-95 359
22 TraesCS4B01G320100 chr1A 88.129 278 28 4 1165 1438 583952236 583951960 2.690000e-85 326
23 TraesCS4B01G320100 chr6B 90.129 233 11 6 1206 1438 716387780 716387560 2.730000e-75 292
24 TraesCS4B01G320100 chr3B 89.256 121 12 1 405 525 115218532 115218651 1.740000e-32 150


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G320100 chr4B 611319246 611322043 2797 True 5168 5168 100.0000 1 2798 1 chr4B.!!$R1 2797
1 TraesCS4B01G320100 chr4D 481882189 481884355 2166 True 1177 1875 87.3835 537 2796 2 chr4D.!!$R2 2259
2 TraesCS4B01G320100 chr5A 660836018 660838179 2161 False 992 1657 84.5950 523 2718 2 chr5A.!!$F3 2195
3 TraesCS4B01G320100 chr2D 121722257 121722780 523 False 691 691 90.5480 1 525 1 chr2D.!!$F1 524
4 TraesCS4B01G320100 chr1D 342160013 342160537 524 False 654 654 89.2250 1 526 1 chr1D.!!$F1 525
5 TraesCS4B01G320100 chr1D 458289177 458289702 525 True 645 645 88.8470 2 527 1 chr1D.!!$R2 525
6 TraesCS4B01G320100 chr1D 20720195 20720719 524 True 573 573 86.5170 1 527 1 chr1D.!!$R1 526
7 TraesCS4B01G320100 chr7A 31059935 31060450 515 False 573 573 86.7170 1 525 1 chr7A.!!$F1 524
8 TraesCS4B01G320100 chr6D 724474 725002 528 True 564 564 86.1420 1 525 1 chr6D.!!$R1 524
9 TraesCS4B01G320100 chr2A 696185713 696186238 525 True 560 560 86.0640 1 525 1 chr2A.!!$R1 524

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
563 585 0.038166 ACACCACCCACCATCATGTC 59.962 55.0 0.00 0.00 0.00 3.06 F
1105 1138 0.031994 GAGCAGACCAGCTAGCTAGC 59.968 60.0 33.96 33.96 46.75 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1787 0.106894 AACTAATCTGCGGGCCTAGC 59.893 55.0 15.26 15.26 0.00 3.42 R
2536 2681 0.109597 GTCCGTTTGCAGCATGAAGG 60.110 55.0 0.00 0.07 39.69 3.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
346 353 4.141965 ATGATGACGGCGGCGACA 62.142 61.111 38.93 36.26 0.00 4.35
371 382 3.452264 GGTGTCGGGTATTAGGGTTTAGT 59.548 47.826 0.00 0.00 0.00 2.24
405 417 5.342525 CGTAACCTAGCGTGATATCATGAAC 59.657 44.000 25.88 11.00 34.90 3.18
407 419 5.276461 ACCTAGCGTGATATCATGAACAA 57.724 39.130 25.88 8.46 34.90 2.83
408 420 5.858381 ACCTAGCGTGATATCATGAACAAT 58.142 37.500 25.88 9.75 34.90 2.71
410 422 7.441836 ACCTAGCGTGATATCATGAACAATAA 58.558 34.615 25.88 4.26 34.90 1.40
412 424 8.939929 CCTAGCGTGATATCATGAACAATAAAT 58.060 33.333 25.88 4.78 34.90 1.40
513 534 7.982371 ATACACGTGTAAATACAGAAGCTAC 57.018 36.000 30.46 0.00 36.78 3.58
527 548 4.218635 CAGAAGCTACACAGTCTAACAGGA 59.781 45.833 0.00 0.00 0.00 3.86
528 549 4.218852 AGAAGCTACACAGTCTAACAGGAC 59.781 45.833 0.00 0.00 36.56 3.85
529 550 2.488545 AGCTACACAGTCTAACAGGACG 59.511 50.000 0.00 0.00 40.76 4.79
530 551 2.415625 GCTACACAGTCTAACAGGACGG 60.416 54.545 0.00 0.00 40.76 4.79
531 552 1.991121 ACACAGTCTAACAGGACGGA 58.009 50.000 0.00 0.00 40.76 4.69
532 553 1.612463 ACACAGTCTAACAGGACGGAC 59.388 52.381 0.00 0.00 40.76 4.79
533 554 1.067776 CACAGTCTAACAGGACGGACC 60.068 57.143 0.00 0.00 40.76 4.46
563 585 0.038166 ACACCACCCACCATCATGTC 59.962 55.000 0.00 0.00 0.00 3.06
611 633 4.052229 CGACAAGCGTCCGTCCCT 62.052 66.667 0.00 0.00 39.11 4.20
713 738 4.754667 GTCGTCGCCCCCAAGTCC 62.755 72.222 0.00 0.00 0.00 3.85
743 768 2.354074 AAAGCAAGCAACACGGCAGG 62.354 55.000 0.00 0.00 35.83 4.85
744 769 3.286751 GCAAGCAACACGGCAGGA 61.287 61.111 0.00 0.00 35.83 3.86
782 807 3.673599 GCGCTGAGCTTTTCCCTT 58.326 55.556 1.78 0.00 44.04 3.95
786 811 1.237285 GCTGAGCTTTTCCCTTCGCA 61.237 55.000 0.00 0.00 0.00 5.10
867 892 2.436646 CGAGCTGGCGATGGGTTT 60.437 61.111 0.00 0.00 0.00 3.27
868 893 2.464459 CGAGCTGGCGATGGGTTTC 61.464 63.158 0.00 0.00 0.00 2.78
869 894 2.044946 AGCTGGCGATGGGTTTCC 60.045 61.111 0.00 0.00 0.00 3.13
903 932 5.276395 CGACGTGGAGAGCAGTAAATAAATG 60.276 44.000 0.00 0.00 0.00 2.32
904 933 4.332819 ACGTGGAGAGCAGTAAATAAATGC 59.667 41.667 0.00 0.00 40.29 3.56
933 962 2.363038 TCGTGAAAGAGAAGGAAACGGA 59.637 45.455 0.00 0.00 0.00 4.69
934 963 3.128349 CGTGAAAGAGAAGGAAACGGAA 58.872 45.455 0.00 0.00 0.00 4.30
935 964 3.059800 CGTGAAAGAGAAGGAAACGGAAC 60.060 47.826 0.00 0.00 0.00 3.62
977 1010 0.535102 CCATCACCAGATAACCCCGC 60.535 60.000 0.00 0.00 31.88 6.13
1043 1076 1.419374 CAGTATATTCACTCGCCGCC 58.581 55.000 0.00 0.00 0.00 6.13
1102 1135 1.001503 AGGAGCAGACCAGCTAGCT 59.998 57.895 12.68 12.68 46.75 3.32
1103 1136 0.260230 AGGAGCAGACCAGCTAGCTA 59.740 55.000 18.86 0.00 46.75 3.32
1104 1137 0.673437 GGAGCAGACCAGCTAGCTAG 59.327 60.000 18.86 16.84 46.75 3.42
1105 1138 0.031994 GAGCAGACCAGCTAGCTAGC 59.968 60.000 33.96 33.96 46.75 3.42
1189 1229 1.150081 CCATGGAGATGGGTGGAGC 59.850 63.158 5.56 0.00 45.11 4.70
1190 1230 1.227764 CATGGAGATGGGTGGAGCG 60.228 63.158 0.00 0.00 0.00 5.03
1194 1234 2.285368 AGATGGGTGGAGCGGGAA 60.285 61.111 0.00 0.00 0.00 3.97
1200 1240 2.579738 GTGGAGCGGGAAGAGGAC 59.420 66.667 0.00 0.00 0.00 3.85
1202 1242 2.754658 GGAGCGGGAAGAGGACGA 60.755 66.667 0.00 0.00 0.00 4.20
1203 1243 2.128507 GGAGCGGGAAGAGGACGAT 61.129 63.158 0.00 0.00 0.00 3.73
1441 1484 3.834799 CCGCCTCGGGACCACTAC 61.835 72.222 0.00 0.00 44.15 2.73
1482 1532 2.791927 CCGAGCGATGAGACACGA 59.208 61.111 0.00 0.00 0.00 4.35
1483 1533 1.356979 CCGAGCGATGAGACACGAT 59.643 57.895 0.00 0.00 0.00 3.73
1485 1535 0.658829 CGAGCGATGAGACACGATCC 60.659 60.000 0.00 0.00 40.92 3.36
1486 1536 0.318275 GAGCGATGAGACACGATCCC 60.318 60.000 0.00 0.00 38.66 3.85
1487 1537 1.658717 GCGATGAGACACGATCCCG 60.659 63.158 0.00 0.00 42.50 5.14
1491 1542 4.570663 GAGACACGATCCCGCCGG 62.571 72.222 0.00 0.00 39.95 6.13
1522 1573 3.049674 CGTGCAGGCATCCACGTT 61.050 61.111 6.67 0.00 46.90 3.99
1523 1574 2.562912 GTGCAGGCATCCACGTTG 59.437 61.111 0.00 0.00 0.00 4.10
1524 1575 3.364441 TGCAGGCATCCACGTTGC 61.364 61.111 2.01 2.01 39.41 4.17
1529 1583 1.154225 GGCATCCACGTTGCTTTCG 60.154 57.895 10.31 0.00 40.03 3.46
1531 1585 1.852067 GCATCCACGTTGCTTTCGGT 61.852 55.000 3.46 0.00 37.14 4.69
1532 1586 0.165944 CATCCACGTTGCTTTCGGTC 59.834 55.000 0.00 0.00 0.00 4.79
1535 1589 2.663852 ACGTTGCTTTCGGTCCCG 60.664 61.111 0.00 0.00 41.35 5.14
1547 1601 0.753262 CGGTCCCGGATTCTTGATCT 59.247 55.000 0.73 0.00 35.02 2.75
1550 1604 1.943340 GTCCCGGATTCTTGATCTTGC 59.057 52.381 0.73 0.00 35.02 4.01
1551 1605 1.839994 TCCCGGATTCTTGATCTTGCT 59.160 47.619 0.73 0.00 35.02 3.91
1560 1614 7.201679 CGGATTCTTGATCTTGCTTGTAAATCT 60.202 37.037 0.00 0.00 35.02 2.40
1578 1637 1.272490 TCTCATTGCGTTTCTCTCGGT 59.728 47.619 0.00 0.00 0.00 4.69
1579 1638 1.656095 CTCATTGCGTTTCTCTCGGTC 59.344 52.381 0.00 0.00 0.00 4.79
1580 1639 0.366871 CATTGCGTTTCTCTCGGTCG 59.633 55.000 0.00 0.00 0.00 4.79
1581 1640 1.352156 ATTGCGTTTCTCTCGGTCGC 61.352 55.000 0.00 0.00 45.70 5.19
1582 1641 2.430244 GCGTTTCTCTCGGTCGCA 60.430 61.111 0.00 0.00 45.01 5.10
1673 1738 2.677836 TGATCGGAATGTAAGCAACAGC 59.322 45.455 0.00 0.00 42.70 4.40
1705 1770 0.975040 AGTGCCGATCTCTCTGCCTT 60.975 55.000 0.00 0.00 31.18 4.35
1707 1772 1.260538 TGCCGATCTCTCTGCCTTGT 61.261 55.000 0.00 0.00 31.18 3.16
1708 1773 0.747255 GCCGATCTCTCTGCCTTGTA 59.253 55.000 0.00 0.00 0.00 2.41
1720 1785 3.053693 TCTGCCTTGTATATTTGGCTGGT 60.054 43.478 14.66 0.00 45.11 4.00
1721 1786 4.165180 TCTGCCTTGTATATTTGGCTGGTA 59.835 41.667 14.66 0.00 45.11 3.25
1722 1787 4.460263 TGCCTTGTATATTTGGCTGGTAG 58.540 43.478 12.05 0.00 45.11 3.18
1723 1788 3.253432 GCCTTGTATATTTGGCTGGTAGC 59.747 47.826 0.00 0.00 41.92 3.58
1751 1816 5.230942 CCCGCAGATTAGTTGGATAAGTAG 58.769 45.833 0.00 0.00 0.00 2.57
1774 1846 2.113289 ACGTACGTGCAATTTTTGTGC 58.887 42.857 22.14 0.00 42.55 4.57
1791 1863 4.278975 TGTGCACAAAGAAAAGGGTTTT 57.721 36.364 19.28 0.00 35.12 2.43
1867 1945 1.079266 GACTGAGTGGCTGGCTGAG 60.079 63.158 2.00 0.00 0.00 3.35
1869 1947 1.123861 ACTGAGTGGCTGGCTGAGAA 61.124 55.000 2.00 0.00 0.00 2.87
1876 1955 1.505477 GGCTGGCTGAGAATGATCGC 61.505 60.000 0.00 0.00 0.00 4.58
1959 2067 2.688507 AGTGTACAGTGCAAGATTCGG 58.311 47.619 1.37 0.00 0.00 4.30
1964 2072 3.678056 ACAGTGCAAGATTCGGTTCTA 57.322 42.857 0.00 0.00 0.00 2.10
1970 2078 5.869888 AGTGCAAGATTCGGTTCTAAAGTAG 59.130 40.000 0.00 0.00 0.00 2.57
1972 2080 6.810182 GTGCAAGATTCGGTTCTAAAGTAGTA 59.190 38.462 0.00 0.00 0.00 1.82
1973 2081 7.009357 GTGCAAGATTCGGTTCTAAAGTAGTAG 59.991 40.741 0.00 0.00 0.00 2.57
1974 2082 7.094075 TGCAAGATTCGGTTCTAAAGTAGTAGA 60.094 37.037 0.00 0.00 0.00 2.59
1975 2083 7.921745 GCAAGATTCGGTTCTAAAGTAGTAGAT 59.078 37.037 0.00 0.00 30.25 1.98
1989 2114 5.444176 AGTAGTAGATTAACCCGTGCTACT 58.556 41.667 0.00 0.00 42.92 2.57
2004 2129 0.460311 CTACTGCTACCCCAGAACGG 59.540 60.000 0.00 0.00 36.67 4.44
2030 2160 0.608035 CGGGGCAGAAGCTGGTTTTA 60.608 55.000 0.00 0.00 41.70 1.52
2034 2164 3.007940 GGGGCAGAAGCTGGTTTTATTTT 59.992 43.478 0.00 0.00 41.70 1.82
2035 2165 4.504864 GGGGCAGAAGCTGGTTTTATTTTT 60.505 41.667 0.00 0.00 41.70 1.94
2137 2279 0.179000 CTCCCCCATGTACTGCACTC 59.821 60.000 0.00 0.00 0.00 3.51
2141 2283 0.179100 CCCATGTACTGCACTCGAGG 60.179 60.000 18.41 6.97 0.00 4.63
2203 2346 1.647545 CGCCTTCAATCATGCACGGT 61.648 55.000 0.00 0.00 0.00 4.83
2208 2351 1.026182 TCAATCATGCACGGTCTGGC 61.026 55.000 0.00 0.00 0.00 4.85
2226 2369 4.544689 CTCCGGCGTCAGCGAGAG 62.545 72.222 6.01 0.00 46.35 3.20
2249 2392 1.616865 ACGGTCGAGATCAACTTGGAA 59.383 47.619 0.00 0.00 0.00 3.53
2253 2396 3.188667 GGTCGAGATCAACTTGGAAAACC 59.811 47.826 0.00 0.00 0.00 3.27
2271 2414 2.174107 CGTGCGTGGCTCAATGTG 59.826 61.111 0.00 0.00 0.00 3.21
2291 2434 0.391130 TGACGCCAATGTCAGTAGGC 60.391 55.000 0.00 0.00 43.62 3.93
2301 2444 1.969589 TCAGTAGGCACGCGTGAGA 60.970 57.895 41.19 22.36 0.00 3.27
2303 2446 1.073216 CAGTAGGCACGCGTGAGAAG 61.073 60.000 41.19 20.70 0.00 2.85
2365 2508 2.182030 CGGTCGTGGGAGAGAAGC 59.818 66.667 0.00 0.00 0.00 3.86
2366 2509 2.579738 GGTCGTGGGAGAGAAGCC 59.420 66.667 0.00 0.00 0.00 4.35
2367 2510 2.182030 GTCGTGGGAGAGAAGCCG 59.818 66.667 0.00 0.00 0.00 5.52
2368 2511 3.760035 TCGTGGGAGAGAAGCCGC 61.760 66.667 0.00 0.00 0.00 6.53
2372 2515 4.537433 GGGAGAGAAGCCGCGCAT 62.537 66.667 8.75 0.00 0.00 4.73
2373 2516 3.267860 GGAGAGAAGCCGCGCATG 61.268 66.667 8.75 0.00 0.00 4.06
2374 2517 2.510238 GAGAGAAGCCGCGCATGT 60.510 61.111 8.75 0.00 0.00 3.21
2375 2518 2.510238 AGAGAAGCCGCGCATGTC 60.510 61.111 8.75 0.00 0.00 3.06
2376 2519 2.510238 GAGAAGCCGCGCATGTCT 60.510 61.111 8.75 3.63 0.00 3.41
2377 2520 2.510238 AGAAGCCGCGCATGTCTC 60.510 61.111 8.75 0.00 0.00 3.36
2378 2521 3.567797 GAAGCCGCGCATGTCTCC 61.568 66.667 8.75 0.00 0.00 3.71
2385 2528 4.776322 CGCATGTCTCCCCCGCAA 62.776 66.667 0.00 0.00 0.00 4.85
2386 2529 2.361104 GCATGTCTCCCCCGCAAA 60.361 61.111 0.00 0.00 0.00 3.68
2387 2530 1.976474 GCATGTCTCCCCCGCAAAA 60.976 57.895 0.00 0.00 0.00 2.44
2388 2531 1.531739 GCATGTCTCCCCCGCAAAAA 61.532 55.000 0.00 0.00 0.00 1.94
2484 2629 4.983628 GCGATGAGCCGATGAGAT 57.016 55.556 0.00 0.00 40.81 2.75
2489 2634 2.668001 CGATGAGCCGATGAGATGAGAC 60.668 54.545 0.00 0.00 0.00 3.36
2493 2638 0.665835 GCCGATGAGATGAGACGAGT 59.334 55.000 0.00 0.00 0.00 4.18
2494 2639 1.874231 GCCGATGAGATGAGACGAGTA 59.126 52.381 0.00 0.00 0.00 2.59
2495 2640 2.350007 GCCGATGAGATGAGACGAGTAC 60.350 54.545 0.00 0.00 0.00 2.73
2504 2649 6.127394 TGAGATGAGACGAGTACAGTAGTAGT 60.127 42.308 1.02 1.02 36.60 2.73
2604 2749 3.350909 AATCGCTGCGCCGTGACTA 62.351 57.895 17.44 0.00 0.00 2.59
2606 2751 4.778415 CGCTGCGCCGTGACTACT 62.778 66.667 9.88 0.00 0.00 2.57
2634 2787 4.317291 CGCTGCTTTTATGTACGTGTTTTC 59.683 41.667 0.00 0.00 0.00 2.29
2757 2914 1.396607 TTCCCTGCCATGCATGCATC 61.397 55.000 30.07 19.96 38.13 3.91
2796 2953 2.887568 CGCACTGGATCGAGCACC 60.888 66.667 1.84 0.77 0.00 5.01
2797 2954 2.265739 GCACTGGATCGAGCACCA 59.734 61.111 1.84 5.82 34.81 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 251 2.272146 GGATTTCTGCCGGCCTCA 59.728 61.111 26.77 3.87 0.00 3.86
259 263 3.198953 TTCCACCACCGCGGGATTT 62.199 57.895 31.76 4.77 40.22 2.17
329 333 4.141965 TGTCGCCGCCGTCATCAT 62.142 61.111 0.00 0.00 35.54 2.45
346 353 1.397390 CCCTAATACCCGACACCGCT 61.397 60.000 0.00 0.00 0.00 5.52
353 360 3.992999 TCCACTAAACCCTAATACCCGA 58.007 45.455 0.00 0.00 0.00 5.14
371 382 1.403249 GCTAGGTTACGTTCGCTTCCA 60.403 52.381 0.00 0.00 0.00 3.53
405 417 4.932799 GTCGGTTCCCCCAAAAATTTATTG 59.067 41.667 0.00 0.00 0.00 1.90
407 419 4.161102 TGTCGGTTCCCCCAAAAATTTAT 58.839 39.130 0.00 0.00 0.00 1.40
408 420 3.573695 TGTCGGTTCCCCCAAAAATTTA 58.426 40.909 0.00 0.00 0.00 1.40
410 422 2.089600 TGTCGGTTCCCCCAAAAATT 57.910 45.000 0.00 0.00 0.00 1.82
412 424 2.892215 GTTATGTCGGTTCCCCCAAAAA 59.108 45.455 0.00 0.00 0.00 1.94
413 425 2.158505 TGTTATGTCGGTTCCCCCAAAA 60.159 45.455 0.00 0.00 0.00 2.44
427 440 3.527665 AGGCCACCCTTAGAATGTTATGT 59.472 43.478 5.01 0.00 38.74 2.29
430 443 4.972568 TGATAGGCCACCCTTAGAATGTTA 59.027 41.667 5.01 0.00 42.87 2.41
434 447 3.393687 TGTGATAGGCCACCCTTAGAAT 58.606 45.455 5.01 0.00 42.87 2.40
440 453 8.884323 CATTATATATATGTGATAGGCCACCCT 58.116 37.037 5.01 0.00 45.61 4.34
513 534 1.067776 GGTCCGTCCTGTTAGACTGTG 60.068 57.143 0.00 0.00 34.46 3.66
553 574 0.677731 CCCGCACAAGACATGATGGT 60.678 55.000 0.00 0.00 0.00 3.55
611 633 3.664888 ATGAAGCAGGGCTGGGCA 61.665 61.111 0.00 0.00 39.62 5.36
705 730 0.689745 TCCTATGACCGGGACTTGGG 60.690 60.000 6.32 9.42 0.00 4.12
707 732 2.906354 CTTTCCTATGACCGGGACTTG 58.094 52.381 6.32 0.00 0.00 3.16
708 733 1.209747 GCTTTCCTATGACCGGGACTT 59.790 52.381 6.32 0.18 0.00 3.01
709 734 0.831307 GCTTTCCTATGACCGGGACT 59.169 55.000 6.32 0.00 0.00 3.85
710 735 0.539986 TGCTTTCCTATGACCGGGAC 59.460 55.000 6.32 0.00 0.00 4.46
711 736 1.209504 CTTGCTTTCCTATGACCGGGA 59.790 52.381 6.32 0.00 0.00 5.14
712 737 1.668419 CTTGCTTTCCTATGACCGGG 58.332 55.000 6.32 0.00 0.00 5.73
713 738 1.017387 GCTTGCTTTCCTATGACCGG 58.983 55.000 0.00 0.00 0.00 5.28
714 739 1.737838 TGCTTGCTTTCCTATGACCG 58.262 50.000 0.00 0.00 0.00 4.79
719 744 1.812571 CCGTGTTGCTTGCTTTCCTAT 59.187 47.619 0.00 0.00 0.00 2.57
743 768 2.223377 CCGCTGTTTCCGGCTAATAATC 59.777 50.000 0.00 0.00 41.05 1.75
744 769 2.218603 CCGCTGTTTCCGGCTAATAAT 58.781 47.619 0.00 0.00 41.05 1.28
855 880 1.839148 TAACCGGAAACCCATCGCCA 61.839 55.000 9.46 0.00 0.00 5.69
856 881 0.677414 TTAACCGGAAACCCATCGCC 60.677 55.000 9.46 0.00 0.00 5.54
903 932 2.127758 CTTTCACGACGCGTTGGC 60.128 61.111 29.09 8.95 38.32 4.52
904 933 0.937699 TCTCTTTCACGACGCGTTGG 60.938 55.000 29.09 19.14 38.32 3.77
1020 1053 0.431233 GCGAGTGAATATACTGCGCG 59.569 55.000 0.00 0.00 37.42 6.86
1021 1054 0.784778 GGCGAGTGAATATACTGCGC 59.215 55.000 0.00 0.00 41.74 6.09
1022 1055 1.053048 CGGCGAGTGAATATACTGCG 58.947 55.000 0.00 0.00 0.00 5.18
1023 1056 0.784778 GCGGCGAGTGAATATACTGC 59.215 55.000 12.98 0.00 0.00 4.40
1043 1076 3.157949 GGGCGGAGGAAGGAGAGG 61.158 72.222 0.00 0.00 0.00 3.69
1114 1148 4.842091 CTTGCTGCGGCGCCATTC 62.842 66.667 30.82 15.29 42.25 2.67
1180 1220 3.003173 CTCTTCCCGCTCCACCCA 61.003 66.667 0.00 0.00 0.00 4.51
1184 1224 2.856039 ATCGTCCTCTTCCCGCTCCA 62.856 60.000 0.00 0.00 0.00 3.86
1189 1229 1.355916 GACGATCGTCCTCTTCCCG 59.644 63.158 33.06 0.00 39.08 5.14
1190 1230 1.094073 TCGACGATCGTCCTCTTCCC 61.094 60.000 35.48 14.75 41.76 3.97
1194 1234 2.172372 CCGTCGACGATCGTCCTCT 61.172 63.158 37.65 8.85 41.76 3.69
1438 1481 2.754375 GGTGGTGGTGGTGGGTAG 59.246 66.667 0.00 0.00 0.00 3.18
1439 1482 2.855014 GGGTGGTGGTGGTGGGTA 60.855 66.667 0.00 0.00 0.00 3.69
1507 1558 3.364441 GCAACGTGGATGCCTGCA 61.364 61.111 0.00 0.00 37.85 4.41
1511 1562 1.154225 CGAAAGCAACGTGGATGCC 60.154 57.895 7.08 0.00 44.91 4.40
1517 1568 2.943653 GGGACCGAAAGCAACGTG 59.056 61.111 0.00 0.00 0.00 4.49
1519 1570 3.419759 CCGGGACCGAAAGCAACG 61.420 66.667 13.13 0.00 42.83 4.10
1520 1571 0.958876 AATCCGGGACCGAAAGCAAC 60.959 55.000 13.13 0.00 42.83 4.17
1521 1572 0.675522 GAATCCGGGACCGAAAGCAA 60.676 55.000 13.13 0.00 42.83 3.91
1522 1573 1.078708 GAATCCGGGACCGAAAGCA 60.079 57.895 13.13 0.00 42.83 3.91
1523 1574 0.392595 AAGAATCCGGGACCGAAAGC 60.393 55.000 13.13 0.00 42.83 3.51
1524 1575 1.066430 TCAAGAATCCGGGACCGAAAG 60.066 52.381 13.13 0.00 42.83 2.62
1529 1583 2.565841 CAAGATCAAGAATCCGGGACC 58.434 52.381 0.00 0.00 34.67 4.46
1531 1585 1.839994 AGCAAGATCAAGAATCCGGGA 59.160 47.619 0.00 0.00 34.67 5.14
1532 1586 2.338577 AGCAAGATCAAGAATCCGGG 57.661 50.000 0.00 0.00 34.67 5.73
1535 1589 7.994194 AGATTTACAAGCAAGATCAAGAATCC 58.006 34.615 0.00 0.00 34.67 3.01
1547 1601 4.764679 ACGCAATGAGATTTACAAGCAA 57.235 36.364 0.00 0.00 0.00 3.91
1550 1604 6.835914 AGAGAAACGCAATGAGATTTACAAG 58.164 36.000 0.00 0.00 0.00 3.16
1551 1605 6.401047 CGAGAGAAACGCAATGAGATTTACAA 60.401 38.462 0.00 0.00 0.00 2.41
1560 1614 1.710013 GACCGAGAGAAACGCAATGA 58.290 50.000 0.00 0.00 0.00 2.57
1578 1637 2.583319 GCTGCTAGTGCGATGCGA 60.583 61.111 0.00 0.00 43.34 5.10
1673 1738 2.510238 GCACTGAGGTAGCGGCAG 60.510 66.667 13.82 13.82 35.81 4.85
1705 1770 4.262894 GCCTAGCTACCAGCCAAATATACA 60.263 45.833 0.00 0.00 43.77 2.29
1707 1772 3.263425 GGCCTAGCTACCAGCCAAATATA 59.737 47.826 16.36 0.00 43.77 0.86
1708 1773 2.040412 GGCCTAGCTACCAGCCAAATAT 59.960 50.000 16.36 0.00 43.77 1.28
1720 1785 1.257743 CTAATCTGCGGGCCTAGCTA 58.742 55.000 20.93 11.82 35.28 3.32
1721 1786 0.760945 ACTAATCTGCGGGCCTAGCT 60.761 55.000 20.93 0.00 35.28 3.32
1722 1787 0.106894 AACTAATCTGCGGGCCTAGC 59.893 55.000 15.26 15.26 0.00 3.42
1723 1788 1.541233 CCAACTAATCTGCGGGCCTAG 60.541 57.143 0.84 0.00 0.00 3.02
1751 1816 3.660356 CACAAAAATTGCACGTACGTACC 59.340 43.478 22.34 15.31 0.00 3.34
1774 1846 4.738252 GCTACGAAAACCCTTTTCTTTGTG 59.262 41.667 0.00 0.00 45.23 3.33
1791 1863 1.000506 GAATAATCTGCGGGGCTACGA 59.999 52.381 6.34 0.00 35.47 3.43
1858 1936 0.532417 AGCGATCATTCTCAGCCAGC 60.532 55.000 0.00 0.00 0.00 4.85
1859 1937 1.500108 GAGCGATCATTCTCAGCCAG 58.500 55.000 0.00 0.00 0.00 4.85
1867 1945 0.528466 TGACTGCCGAGCGATCATTC 60.528 55.000 0.00 0.00 0.00 2.67
1869 1947 1.067084 CTGACTGCCGAGCGATCAT 59.933 57.895 0.00 0.00 0.00 2.45
1876 1955 1.214062 GGACTGTCTGACTGCCGAG 59.786 63.158 13.73 2.92 0.00 4.63
1959 2067 7.221645 GCACGGGTTAATCTACTACTTTAGAAC 59.778 40.741 0.00 0.00 31.78 3.01
1964 2072 5.672421 AGCACGGGTTAATCTACTACTTT 57.328 39.130 0.00 0.00 0.00 2.66
1970 2078 3.121544 GCAGTAGCACGGGTTAATCTAC 58.878 50.000 0.00 0.00 41.58 2.59
1972 2080 1.831736 AGCAGTAGCACGGGTTAATCT 59.168 47.619 0.00 0.00 45.49 2.40
1973 2081 2.311124 AGCAGTAGCACGGGTTAATC 57.689 50.000 0.00 0.00 45.49 1.75
1974 2082 2.159000 GGTAGCAGTAGCACGGGTTAAT 60.159 50.000 0.00 0.00 45.49 1.40
1975 2083 1.205417 GGTAGCAGTAGCACGGGTTAA 59.795 52.381 0.00 0.00 45.49 2.01
1989 2114 2.925706 TGCCGTTCTGGGGTAGCA 60.926 61.111 0.00 0.00 38.63 3.49
2070 2200 0.184211 TACATGGGGAGGTCGATCGA 59.816 55.000 15.15 15.15 0.00 3.59
2221 2364 2.381665 GATCTCGACCGTGCCTCTCG 62.382 65.000 0.00 0.00 0.00 4.04
2224 2367 0.802607 GTTGATCTCGACCGTGCCTC 60.803 60.000 0.00 0.00 0.00 4.70
2225 2368 1.215647 GTTGATCTCGACCGTGCCT 59.784 57.895 0.00 0.00 0.00 4.75
2226 2369 0.389948 AAGTTGATCTCGACCGTGCC 60.390 55.000 0.00 0.00 0.00 5.01
2227 2370 0.716108 CAAGTTGATCTCGACCGTGC 59.284 55.000 0.00 0.00 0.00 5.34
2228 2371 1.067846 TCCAAGTTGATCTCGACCGTG 60.068 52.381 3.87 0.00 0.00 4.94
2229 2372 1.254026 TCCAAGTTGATCTCGACCGT 58.746 50.000 3.87 0.00 0.00 4.83
2230 2373 2.363788 TTCCAAGTTGATCTCGACCG 57.636 50.000 3.87 0.00 0.00 4.79
2231 2374 3.188667 GGTTTTCCAAGTTGATCTCGACC 59.811 47.826 3.87 1.34 40.31 4.79
2232 2375 3.188667 GGGTTTTCCAAGTTGATCTCGAC 59.811 47.826 3.87 0.00 42.91 4.20
2233 2376 3.408634 GGGTTTTCCAAGTTGATCTCGA 58.591 45.455 3.87 0.00 42.91 4.04
2234 2377 2.159627 CGGGTTTTCCAAGTTGATCTCG 59.840 50.000 3.87 0.00 42.91 4.04
2249 2392 4.555709 TGAGCCACGCACGGGTTT 62.556 61.111 0.00 0.00 36.74 3.27
2253 2396 3.049674 ACATTGAGCCACGCACGG 61.050 61.111 0.00 0.00 0.00 4.94
2271 2414 1.359848 CCTACTGACATTGGCGTCAC 58.640 55.000 0.00 0.00 40.94 3.67
2288 2431 3.616721 ACCTTCTCACGCGTGCCT 61.617 61.111 33.63 9.13 0.00 4.75
2291 2434 1.591594 ACACACCTTCTCACGCGTG 60.592 57.895 32.76 32.76 0.00 5.34
2301 2444 0.958382 AACACGCACACACACACCTT 60.958 50.000 0.00 0.00 0.00 3.50
2303 2446 1.226267 CAACACGCACACACACACC 60.226 57.895 0.00 0.00 0.00 4.16
2368 2511 4.776322 TTGCGGGGGAGACATGCG 62.776 66.667 0.00 0.00 0.00 4.73
2369 2512 1.531739 TTTTTGCGGGGGAGACATGC 61.532 55.000 0.00 0.00 0.00 4.06
2370 2513 2.652313 TTTTTGCGGGGGAGACATG 58.348 52.632 0.00 0.00 0.00 3.21
2392 2535 1.244019 ATGCGCGGCTTCTCCTTTTT 61.244 50.000 8.83 0.00 0.00 1.94
2393 2536 1.675641 ATGCGCGGCTTCTCCTTTT 60.676 52.632 8.83 0.00 0.00 2.27
2394 2537 2.045926 ATGCGCGGCTTCTCCTTT 60.046 55.556 8.83 0.00 0.00 3.11
2395 2538 2.821366 CATGCGCGGCTTCTCCTT 60.821 61.111 8.83 0.00 0.00 3.36
2396 2539 4.087892 ACATGCGCGGCTTCTCCT 62.088 61.111 8.83 0.00 0.00 3.69
2397 2540 3.567797 GACATGCGCGGCTTCTCC 61.568 66.667 8.83 0.00 0.00 3.71
2398 2541 2.510238 AGACATGCGCGGCTTCTC 60.510 61.111 8.83 0.00 0.00 2.87
2399 2542 2.510238 GAGACATGCGCGGCTTCT 60.510 61.111 8.83 1.02 0.00 2.85
2400 2543 3.918220 CGAGACATGCGCGGCTTC 61.918 66.667 8.83 0.00 36.08 3.86
2401 2544 4.742201 ACGAGACATGCGCGGCTT 62.742 61.111 8.83 0.00 44.49 4.35
2475 2618 2.872858 TGTACTCGTCTCATCTCATCGG 59.127 50.000 0.00 0.00 0.00 4.18
2476 2619 3.558006 ACTGTACTCGTCTCATCTCATCG 59.442 47.826 0.00 0.00 0.00 3.84
2479 2624 5.087391 ACTACTGTACTCGTCTCATCTCA 57.913 43.478 0.00 0.00 0.00 3.27
2484 2629 7.148507 GCTAAAACTACTACTGTACTCGTCTCA 60.149 40.741 0.00 0.00 0.00 3.27
2489 2634 6.099579 TCGCTAAAACTACTACTGTACTCG 57.900 41.667 0.00 0.00 0.00 4.18
2493 2638 4.096984 GGCCTCGCTAAAACTACTACTGTA 59.903 45.833 0.00 0.00 0.00 2.74
2494 2639 3.119209 GGCCTCGCTAAAACTACTACTGT 60.119 47.826 0.00 0.00 0.00 3.55
2495 2640 3.445857 GGCCTCGCTAAAACTACTACTG 58.554 50.000 0.00 0.00 0.00 2.74
2504 2649 1.375013 GACGTGGGCCTCGCTAAAA 60.375 57.895 26.31 0.00 0.00 1.52
2536 2681 0.109597 GTCCGTTTGCAGCATGAAGG 60.110 55.000 0.00 0.07 39.69 3.46
2540 2685 1.130955 GTTTGTCCGTTTGCAGCATG 58.869 50.000 0.00 0.00 40.87 4.06
2698 2855 3.512329 ACTTGGACGGTCAAAAACCTTTT 59.488 39.130 10.76 0.00 46.87 2.27
2719 2876 0.460284 ACTGGATGCGAATCCACGAC 60.460 55.000 22.06 0.00 45.19 4.34


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.